1. Experiment Health for: MaxQuant LFQ HER2

The experiment contains 6 samples; the condition of interest has 2 categories: AZD8931_resistant_SKBR3_AZDRc, Parental_SKBR3.

A.Dimensionality reduction

The data have been log2 transformed and imputed using the MNAR imputation method before PCA.

PCA

MDS

B. Quantitative values CV distributions

2. Intensity distribution across runs

Imputed data

Initial data

3. Feature completedness

By sample

By protein

4. Imputed versus non imputed log2 Intensity values

5. Model QC

Volcano plots

MA plot

Histogram of pvalues

## $breaks
##  [1] 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
## 
## $counts
##  [1] 1284   93   74   25   42   31   21   28   30   27
## 
## $density
##  [1] 7.7583082 0.5619335 0.4471299 0.1510574 0.2537764 0.1873112 0.1268882 0.1691843 0.1812689 0.1631420
## 
## $mids
##  [1] 0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95
## 
## $xname
## [1] "stats[, pval]"
## 
## $equidist
## [1] TRUE
## 
## attr(,"class")
## [1] "histogram"